title: HDAC9 WT ChIP

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

institute: Università degli Studi di Udine

description: HDAC9 bound regions

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.1.1 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2 as a BED6+4 format file containing the peak locations together with peak summit, pvalue and qvalue; Scores represet: chr, start, end, peak name, score, strand, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start

growth_protocol: SK-UT-1 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine and penicillin–streptomycin (Euroclone, Milan, Italy). For each ChIP, 3.2*10^6 cells were used.

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with protein A/antibodies (2μg of anti-H3K27ac (Abcam ab4729) , 2.5 μg of anti-MEF2D (BD Bioscience), 4μg of anti-HDAC4 (Paroni et al, 2004) and anti-HDAC9 (home-made antibody) antibodies or control IgG. Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
TruSeq ChIP Library

treatment_protocol: Cells were seeded in 200 mm plate three days before the ChIP. At the moment of the ChIP, cross-linking was performed for 15' with 1% formaldeyde (Fisher Scientific, Schwerte, Germany) and then blocked with 125 mM Glycine (Sigma-Aldrich, Darmstadt, Germany).

value: Leiomyosarcoma cells

value: below 20

tag: chip antibody

value: HDAC9 (Di Giorgio et al, 2019 NAR submitted)


title: MEF2D WT ChIP

status: Public on Nov 12 2019

type: SRA

country: Italy

description: MEF2D bound regions

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: passages

tag: strain

value: MEF2D (BD Biosciences, clone 9 610775)


title: HDAC4 WT ChIP

description: HDAC4 bound regions

value: HDAC4 (Paroni et al, 2004 PMID 15075374 )


title: Prostate: HMN_PC_089

city: Paris

first: Marina

last: Pinskaya

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: total ribo-depleted RNA

library_source: transcriptomic

data_processing:
Reads were mapped with tophat version 2.0.6, with the following parameters : -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 –no-coverage-search --library-type fr-firststrand.
Only unique mapped reads were kept for further analysis.
Read counting was performed using featureCounts version 1.6.0, for the alignment file of each sample, on the annotation gencode27lift37 (using the “gene_id”) and on the new discovered contigs (both annotations put in the same file in SAF-format, as described by the requirements of the program), with the following parameters : -F "SAF" -p -s 2 -O.
Differential expression analysis was performed using Deseq2 version 1.18.1, with default options (genes with 0 count in all samples were preliminarily removed, then a pseudocount of “1” was added).
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, tab-delimited text file of raw counts (the first column is the gene ID, and the second column is the raw count value)

molecule: total RNA

source_name: prostate

growth_protocol: Tumor and normal biopsy specimens were obtained from prostate cancer patients who provided informed consent and were approved for collection and distribution by Mondor institutional board.

extract_protocol:
Total RNA was extracted using Trizol, according to manufacturer’s procedure, quantified and quality controlled using a 2100 Bioanalyzer (Agilent). RNA samples with RNA Integrity Number (RIN) above 6 were depleted for ribosomal RNA and converted into cDNA library using a TruSeq Stranded Total Library Preparation kit (Illumina). cDNA libraries were normalized using an Illumina Duplex-specific Nuclease (DSN) protocol prior to a paired-end sequencing on HiSeq™ 2500 (Illumina).
Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2201, Illumina)

tag: tissue

value: prostate tumor

tag: gleason score(prostatoctomy)

tag: tnm score


title: thyroid_cancer_N1b [PTMC8]

type: RNA

city: Seoul

first: Sohee

last: Lee

address: 222 BANPO-DAERO, SEOCHO-GU

department: Surgery

country: South Korea

institute: The Catholic University of Korea

hyb_protocol: Illumina HumanHT-12 v4.0 Expression Beadchip is a direct hybridization assay and targets more than 47000 human probes.   After fragmentation, 750 ng of labeled cRNA samples were hybridized to each HumanHT-12 v4.0 Expression Beadchip for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc.; San Diego, CA, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences; Little Chalfont, UK) following the bead-array manual.   Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: We applied a filtering criterion for data analysis, as a higher signal value was required for detection of p-values of < 0.05. Array probes that have detection p≥0.05 (similar to signal-to-noise ratio) in over 50% of the samples were filtered out (25,391 probes).   Selected gene signal values (for 21,927 probes) were transformed by logarithm and normalized by the quantile method.

label: biotin

source_name: papillary thyroid cancer

label_protocol: Total RNA was amplified and purified using the TargetAmpTM-Nano Labeling Kit for Illumina® Expression BeadChip® (EPICENTRE; Madison, WI, USA) to yield biotinylated cRNA, according to the manufacturer’s instructions.   Briefly, in the range of 200500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo (dT) primer. Second-strand cDNA was synthesized, in-vitro transcribed, and labeled with biotin-NTP.   After purification, the cRNA was quantified spectrophotometrically.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies; Carlsbad, CA, USA) and purified using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturers’ protocols.   The RNA samples were quantified, aliquoted, and stored at -80°C until use. Purity and integrity of RNA was evaluated by denaturing gel electrophoresis and absorbance.   Absorbance measurements at 260 nm were used to quantify RNA (ND-1000 Spectrophotometer) (NanoDrop; Wilmington, DE, USA).  The ratio of absorbance at 260 nm to that at 280 and 230 nm was used as an indication of sample purity, and values of 1.72.0 were considered to indicate relatively pure RNA.   Total-RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA, USA) with an RNA Integrity Number value.

treatment_protocol: We obtained matched thyroid tumor and normal tissues from eight papillary thyroid microcaricinoma patients who underwent thyroidectomy.

tag: disease

value: papillary thyroid cancer, T3N1b


title: Prostate: HMN_PC_228

description: total ribo-depleted RNA


title: Prostate: HMN_PC_102

description: total ribo-depleted RNA


title: H3K27ac H9KO ChIP

description: Open chromatin evaluation in HDAC9KO cells

value: H3K27ac (Abcam, ab4729)


title: Adipocytes alone rep1

city: Shanghai

first: Zhiwei

last: Cai

state: Shanghai

address: Yan'an Road 221

department: Department of Surgery

country: China

institute: Huadong Hospital of Fudan University

data_processing:
The raw reads were trimmed and quality controlled by SeqPrep  and Sickle  with default parameters.
The clean reads were separately aligned to reference genome with orientation mode using bowtie2 software
The expression level for each gene was calculated using the fragments per kilobase of transcript per millions base pairs sequenced (FPKM) method
Genome_build: mm10

organism: Mus musculus

growth_protocol: The 3T3-L1 preadipocytes were cultured in DMEM with 10% newborn calf serum. Two days after 100% of conﬂuence (designated Day 0), 3T3-L1 preadipocytes were induced to differentiate in DMEM containing 10% FBS, 0.5 mM 3-isobutyl-1-methylxanthine (M), 1 μM dexamethasone (D), 1 μg/ml insulin (I) for 2 days. After 48h (Day 2), these cells were sustained in DMEM with 10% FBS and 1 ug/ml insulin for another 2 days. Then, 3T3-L1 mature adipocytes were cultured in DMEM with 10% FBS.

extract_protocol:
Total RNA was extracted from 3T3-L1 mature adipocytes using TRIzol reagent. Genomic DNA was removed using DNase I.
The RNA-seq libraries were prepared according to TruSeqTM RNA sample preparation Kit from Illumina

tag: cell line

tag: treatment

value: control

value: fibroblast


title: H3K27ac H4KO ChIP

description: Open chromatin evaluation in HDAC4KO cells


title: thyroid_normal [PTMC7 matched normal]

description:
matched normal tissue of sample13
27_2.AVG_Signal

source_name: normal thyroid

value: normal thyroid


title: thyroid_normal [PTMC6 matched normal]

description:
matched normal tissue of sample11
23_2.AVG_Signal


title: KO_Ly6C_2

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description:
cKO2 Spleen Ly6C
RHM6011

data_processing:
Paired-end reads were mapped to GRCm38 reference genome using STAR version 2.3
Mapped paired-end reads were summarized to gene level using featureCounts v.1.5.0 and with GENCODE GRCm38 vM15 gene annotation
log2 transformed RPKM values were computed in R version 3.3.3 using edgeR Bioconductor package
Genome_build: GRCm38 / mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level log2 transformed FPKM values for all samples

source_name: spleen

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit according to manufacturer's protocol
cDNA libraries were prepared using 2 ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls using the SMARTSeq v2 protocol. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (25 samples/lane).

value: spleen

tag: genotype

value: CD11c-cre Adam10fl/fl


title: KO_Ly6C_1

description:
cKO1 Spleen Ly6C
RHM6010


title: H3K27ac WT ChIP

description: Open chromatin evaluation in wt cells


title: thyroid_cancer_N1b [PTMC7]


title: thyroid_cancer_N1b [PTMC5]

value: papillary thyroid cancer, T1aN1b


title: thyroid_cancer_N1b [PTMC6]


title: KO_DN_3

description:
cKO3 Spleen DN
RHM6009


title: thyroid_normal [PTMC5 matched normal]

description:
matched normal tissue of sample9
17_2.AVG_Signal


title: Input H9KO

description: Input


title: Input H4KO

description: Input


title: thyroid_normal [PTMC4 matched normal]

description:
matched normal tissue of sample7
10-1.AVG_Signal


title: C8.SHP.1_1

city: La Jolla

first: Nathan

middle: E

last: Lewis

state: California

address: 9500 Gilman Dr

department: Pediatrics

country: USA

institute: UCSD

data_processing:
Alignment and quantification performed using Salmon 0.14.1 default parameters.
tximportData_1.10.0 was used to summarize from transcripts outputted from salmon to gene level counts.
DESeq2 performed for differential expression analysis across genotypes.
K-means clustering performed using the scipy stats module.
Gene-set enrichment analysis was done to determine enriched gene sets across different transcriptional clusters.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Counts matrix, n-by-m matrix, where n is the number of genes, and m is the number of samples. Each column has a header that names after the title column above. This is the gene-wise summarized raw counts from tximportData_1.10.0 .

source_name: Casp8∆PMN Ptpn6∆PMN_bone marrow neutrophils

extract_protocol:
Murine bone marrow cells were isolated from the femur, tibia, and ossa coxae in Hanks Balanced Salt Solution supplemented with 1% fetal bovine serum (FBS) and 15 mM EDTA. Cells were overlayed on 78%, 68% and 52% Percoll layers and centrifuged at 400 × g for 30 min at 4 °C. Neutrophils were removed from the 68%/78% interface and re-suspended in DMEM/10% FBS for sequencing.
RNA was extracted from bone marrow neutrophils according to the manufacturer’s instructions (Qiagen). Paired-end sequencing was performed by BGI Americas, enriching for mRNA, and read lengths were 100 base pairs

tag: strain background

tag: genotype/variation

value: Casp8{delta}PMN Ptpn6{delta}PMN

tag: age

tag: Sex

value: Female

value: bone marrow neutrophils

tag: inflamed

value: Yes


title: thyroid_normal [PTMC3 matched normal]

description:
matched normal tissue of sample5
8-2.AVG_Signal


title: APCKJ1 2-FL vs Lactose Dye Swap

city: Cork

first: Kieran

last: James

address: Biosciences Institute, Gaol Cross, Western Road

department: Microbiology

country: Ireland

institute: APC Microbiome Institute, University College Cork

description: Biological replicate 2

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).  Data processing  DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 2-FL or 3-FL/sorbitol or lactose, or  2-FL or lactose/ribose ratios from a single array experiment.

organism: Bifidobacterium catenulatum subsp. kashiwanohense

source_name: Bifidobacterium kashiwanohense APCKJ1

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: B. kashiwanohense APCKJ1 and Bifidobacterium breve UCC2003-fucA1-fucT cultures were grown separately in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of 2'-fucosyylactose (2-FL), 3'-fucosyllactose (3-FL), Lactose, Sorbitol or Ribose as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) untill OD600 was 0.5.  Growth protocol  Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (Pokusaeva et al., 2009)(van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, 2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: growth media

value: Lactose


title: thyroid_cancer_N1b [PTMC4]


title: Input WT

description: Input

value: Leiomyosarcoma cells

value: below 20

tag: chip antibody


title: KO_DN_2

description:
cKO2 Spleen DN
RHM6008

tag: cell type


title: R3.M.C8.SHP.1_1

source_name: Ripk3-/- Mlkl-/- Casp8∆PMN Ptpn6∆PMN_bone marrow neutrophils

value: Ripk3-/- Mlkl-/- Casp8{delta}PMN Ptpn6{delta}PMN

value: No


title: WT_Ly6C_3

description:
WT3 Spleen Ly6C
RHM6006

value: WT


title: SW480-siPOLR1D-3-3

city: Graz

first: Samantha

last: Perakis

address: Neue Stiftingtalstraße 6

country: Austria

institute: Diagnostic & Research Institute of Human Genetics; MedUniGraz

data_processing:
Illumina Nextseq 550 reas quality was checked for each sample using FastQC v0.11.5.
Pseudoalignment and transcript quantification are done with kallisto 0.44.0.
Normalization of read counts for each gene and RNA abundance analysis were done in R (DESeq2_1.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 normalized counts for each sample .

extract_protocol:
RNA was harvested using Trizol reagent and isolated according to the manufacturer's instructions.
Illumina TruSeq RNA Exome Sample Prep Kit (Cat#FC-122-1001) was used with 1μg of total RNA for the construction of sequencing libraries. More specifically, total RNA libraries were prepared with TruSeq RNA Library Prep for Enrichment kit (Cat. No. 20020189) and transcriptome enrichment was performed with TruSeq RNA Enrichment kit (Cat. No. 20020490),

value: Colorectal cancer cell line

tag: transfection


title: APCKJ1 3-FL vs Sorbitol Dye Swap

description: Biological replicate 2

value: Sorbitol


title: APCKJ1 2-FL vs Lactose

description: Biological replicate 1


title: APCKJ1 2-FL vs Sorbitol Dye Swap

description: Biological replicate 2


title: KO_DN_1

description:
cKO1 Spleen DN
RHM6007

tag: strain


title: M.C8.SHP.1_2

source_name: Casp8∆PMN Mlkl-/- Ptpn6∆PMN_bone marrow neutrophils

value: Casp8{delta}PMN Mlkl-/- Ptpn6{delta}PMN


title: SW480-siPOLR1D-3-2

tag: tissue


title: thyroid_cancer_N0 [PTMC3]

value: papillary thyroid cancer, T1aN0


title: APCKJ1 2-FL vs Sorbitol

description: Biological replicate 1


title: APCKJ1 3-FL vs Sorbitol

description: Biological replicate 1


title: thyroid_normal [PTMC2 matched normal]

description:
matched normal tissue of sample3
4-2.AVG_Signal

value: normal thyroid


title: SW480-siPOLR1D-3-1


title: M.C8.SHP.1_1


title: R3.M.C8.SHP.1_2


title: WT_DN_3

description:
WT3 Spleen DN
RHM6003

value: spleen


title: thyroid_cancer_N0 [PTMC1]


title: WT_Ly6C_2

description:
WT2 Spleen Ly6C
RHM6005


title: R3.M.SHP.1_3

source_name: Ripk3-/- Mlkl-/- Ptpn6∆PMN_bone marrow neutrophils

value: Ripk3-/- Mlkl-/- Ptpn6{delta}PMN


title: WT_DN_2

description:
WT2 Spleen DN
RHM6002


title: SW480-siPOLR1D-2-3


title: R3.M.SHP.1_2


title: thyroid_cancer_N0 [PTMC2]


title: R3.M.SHP.1_1


title: WT_DN_1

description:
WT1 Spleen DN
RHM6001


title: exp2-OTS514

city: Chicago

first: Andrzej

last: Jakubowiak

state: IL

address: 900 E 57th St

department: Medicine

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile Normalization, BeadStudio

source_name: H929 cells

label_protocol: Standard Illumina protocol

growth_protocol: RPMI+10%FCS, 10%CO2

extract_protocol: Qiagen RNeasy mini

treatment_protocol: Drugs applied at indicated concentrations with maximum 0.015%DMSO

tag: replicate


title: SW480-siPOLR1D-2-1


title: exp1-OTS514 CFZ

value: OTS514 CFZ


title: SW480-siPOLR1D-2-2


title: R3.M_2

source_name: Ripk3-/- Mlkl-/-_bone marrow neutrophils

value: Ripk3-/- Mlkl-/-

value: Female


title: Zfc3h1_KO_2_ESC_SUZ12_ChIPseq

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
ChIPseq reads were aligned to mm10 using Bowtie, selecting only hits with the best stratum with up to two mismatches in the seed and reporting up to four good alignments per read
For visualization, ChIPseq reads were shifted to the centre of their fragment by half of fragment size deduced from the ChIP-Cor tool
SUZ12 peaks were called using MACS2 (version 2.1.1.20160309) with parameters --qvalue 0.05 --broad --broad-cutoff 0.3, ENCODE blacklisted peaks (Consortium, 2012) and low quality peaks (-log10(qvalue) ≤ 1) were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: ChIPseq reads bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: RIPseq reads bigwig files were generated using bamCoverage from deepTools (Ramírez et al., 2014), the score represents strand-specific per-base genome coverage which was normalized to the library size

growth_protocol: ES cells were cultured on 0.2% gelatin coated plates in 2i/LIF containing medium.

extract_protocol:
ES cells were cross-linked by the addition of 1% formaldehyde for 10 minutes at RT before quenching with glycine. DNA was sheared to ~ 200 bp fragments by sonication using a Biorupter (Diagenode). ChIPs were carried out using 200 µg of chromatin and 2-3 µg of the indicated antibodies
ChIPseq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) using AmpureXP beads (Beckman) for size selection.

value: Embryonic stem cells

tag: chip/rip antibody


title: SW480-SCR-4

value: SCR


title: Zfc3h1_KO_3_ESC_SUZ12_ChIPseq


title: Zfc3h1_KO_1_ESC_SUZ12_ChIPSeq


title: M.SHP.1_2

source_name: Mlkl-/- Ptpn6∆PMN_bone marrow neutrophils

value: Mlkl-/- Ptpn6{delta}PMN

value: bone marrow neutrophils


title: SW480-SCR-6


title: thyroid_normal [PTMC1 matched normal]

description:
matched normal tissue of sample1
1-2.AVG_Signal

tag: disease


title: Zfc3h1_KO_3_ESC_H3K27me3_ChIPseq

tag: cell line


title: SW480-SCR-2


title: SW480-SCR-3


title: exp3-OTS514 CFZ

tag: treatment


title: exp3-OTS514 LEN

value: OTS514 LEN


title: exp1-LEN CFZ

value: LEN CFZ


title: R3.M_3

value: No


title: R3.M_1


title: SW480-SCR-1

value: Colorectal cancer cell line


title: exp1-LEN

value: LEN


title: exp2-OTS514 CFZ


title: exp1-OTS514 LEN


title: exp3-OTS514 LEN CFZ

value: OTS514 LEN CFZ


title: SW480-SCR-5


title: Zfc3h1_KO_1_ESC_H3K27me3_ChIPseq


title: HT29-siPOLR1D-3-2


title: Zfc3h1_KO_1_ESC_H3K27ac_ChIPseq


title: Zfc3h1_KO_1_ESC_H3K4me3_ChIPseq


title: M_1

source_name: Mlkl-/-_bone marrow neutrophils

value: Mlkl-/-


title: exp1-CFZ

value: CFZ


title: R3.SHP.1_3

source_name: Ripk3-/- Ptpn6∆PMN_bone marrow neutrophils

value: Ripk3-/- Ptpn6{delta}PMN


title: HT29-siPOLR1D-2-2


title: exp3-DMSO

value: DMSO


title: R3.SHP.1_2


title: M_3


title: M.SHP.1_1


title: Zfc3h1_KO_2_ESC_H3K27me3_ChIPseq


title: HT29-siPOLR1D-2-1


title: HT29-SCR-4


title: M_2


title: R3.SHP.1_1


title: HT29-SCR-3


title: R3_3

source_name: Ripk3-/-_bone marrow neutrophils


title: R3_2


title: HT29-siPOLR1D-3-1


title: WT_1_ESC_SUZ12_ChIPSeq

value: Wildtype


title: WT_1_ESC_H3K27me3_ChIPseq


title: WT_1_ESC_H3K27ac_ChIPseq


title: R3_1


title: Zfc3h1_KO_1_ESC_H3K4me1_ChIPseq


title: HT29-SCR-1


title: exp3-LEN CFZ


title: WT_1_ESC_H3K4me1_ChIPseq


title: C57BL6J_3

source_name: wild-type_bone marrow neutrophils

value: wild-type


title: WT_1_ESC_H3K4me3_ChIPseq


title: exp2-DMSO


title: C57BL6J_2

value: Female


title: exp1-DMSO


title: exp1-OTS514 LEN CFZ


title: exp2-LEN CFZ


title: exp1-OTS514


title: exp3-LEN


title: C57BL6J_1


title: WT_1_ESC_input

value: Embryonic stem cells


title: HT29-SCR-2

value: SCR


title: Zfc3h1_KO_2_ESC_EZH2_RIPseq

data_processing:
Quality control of RIPseq reads were done using FastQC v0.11.2 , reads were trimmed using Trim Galore (version: 0.4.4) with parameters -q 20  --length 25 --clip_R1 13 --clip_R2 13 --three_prime_clip_R1 1 --three_prime_clip_R2 1
RIPseq reads were aligned to mm10 using HISAT v0.1.6.beta with --rna-strandness RF --minins 0 --maxins 1000  and a list of GENCODE M12 annotated splice
Uniquely mapped and properly paired reads were selected using SAMtools (version 1.6-1)  and duplicated reads were removed using MarkDuplicates (version: 2.8.1)
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: ChIPseq reads bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: RIPseq reads bigwig files were generated using bamCoverage from deepTools (Ramírez et al., 2014), the score represents strand-specific per-base genome coverage which was normalized to the library size

extract_protocol:
Whole cell native IPs were performed using SUZ12 or EZH2 antibodies and RNA was isolated using Trizol. Total RNA was isolated from input samples in parallel using Trizol.
RIPseq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following rRNA depletion.


title: Zfc3h1_KO_1_ESC_EZH2_RIPseq


title: UCC2003-fucA1-fucT Lactose vs Ribose Dye Swap

description: Biological replicate 2

organism: Bifidobacterium breve UCC2003

value: Lactose

value: Ribose


title: UCC2003-fucA1-fucT 2-FL vs Ribose Dye Swap

description: Biological replicate 2


title: Zfc3h1_KO_2_ESC_SUZ12_RIPseq


title: Zfc3h1_KO_1_EB_D7_RNAseq

data_processing:
Quality control of RNAseq reads were done using FastQC v0.11.2 , reads were trimmed using Trimmomatic v0.32 with settings  “ILLUMINACLIP:<TrueSeq3_PE_2>:2:30:10 HEADCROP:12 LEADING:22 SLIDINGWINDOW:4:22 MINLEN:25”
RNAseq reads were aligned to mm10 using HISAT v0.1.6.beta with --rna-strandness RF --minins 0 --maxins 1000  and a list of GENCODE M12 annotated splice sites was also provided.
Paired and uniquely mapped exonic reads for GENCODE M12 genes were counted using featureCounts from the R package Rsubread (1.32.1)
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: ChIPseq reads bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: RIPseq reads bigwig files were generated using bamCoverage from deepTools (Ramírez et al., 2014), the score represents strand-specific per-base genome coverage which was normalized to the library size

growth_protocol: Embryoid bodies were formed by seeding dissociated ES cells into serum-LIF media (GMEM + 10% FBS) on low attachment petri dishes and grow for 7 days. Media was replaced every 2 days.

extract_protocol:
Total RNA for RNAseq  was isolated using the RNeasy Mini Kit (Qiagen)
RNAseq libraries were prepared from 1 µg RNA using the TruSeq Stranded Total RNA library prep kit (Illumina) following rRNA depletion using Ribozero Gold (Illumina)

value: Embryoid bodies


title: UCC2003-fucA1-fucT Lactose vs Ribose

description: Biological replicate 1


title: UCC2003-fucA1-fucT 2-FL vs Ribose

description: Biological replicate 1


title: Zfc3h1_KO_3_EB_D7_RNAseq


title: exp2-OTS514 LEN

value: OTS514 LEN


title: 12hr_DMSO

city: Pullman

first: Roberta

middle: M

last: O'Connor

state: WA

address: 100 Dairy Road

institute: Washington State University College of Vet Med

data_processing:
75 million to 95 million reads per sample which was analyzed using TopHat-Cufflinks pipeline.
Bases were called with bcl2fastq
Reads were mapped to the T. gondii GT1 genome using Tophat, multi-read correction enabled
The expression level was estimated with Cuffdiff and represented as fragments per kilobase of exons per million mapped fragments (FPKM) to T. gondii GT1 genome available on ToxoDB (Gajria et al., 2008) (http://toxodb.org).
Genome_build: T. gondii GT1 genome available on ToxoDB (Gajria et al., 2008)
Supplementary_files_format_and_content: Microsoft Excel Worksheet that includes RPKM values for each sample, Log2(fold difference) for each gene for all possible comparisons between the samples, and p and q values to identify genes that were significantly differentially expressed between samples.

organism: Toxoplasma gondii RH

source_name: T. gondii infected HFF

growth_protocol: T. gondii was propagated in HFF cells following standard procedures (Roos et al, 1994, Methods Cell Biol 45:27-63).

extract_protocol:
Total RNA was isolated from infected, treated cells with Qiagen's RNeasy kit
The integrity and quantity of total RNA samples were determined by Fragment Analyzer (AATI, Ames, IA, USA). The total RNA samples that satisfied the input requirement were used as input for Illumina TruSeq Stranded Total RNA with Ribo-Zero® Gold sample preparation kit (Illumina, San Diego, CA, USA)

treatment_protocol: TrtE was diluted to a final concetration of 6 or 24.2 nM in HFF culture media and added to HFF cells that had been infected with T. gondii RH stratin 24 hours before.  The vehicle control consisted of DMSO diluted in media to the same dilution used to make the 24.2 nM TrtE (1:50,000). Total RNA was collected from saples after 4, 8 and 12 hours of treatment.

value: human foreskin fibroblast cells (HFF)

tag: parasite life cycle stage

value: intracellular tachyzoites

value: DMSO (vehicle)

tag: length of treatment

value: 12 hours


title: exp3-OTS514


title: 12hr_20ng

value: 24.2 nM TrtE


title: WT_3_EB_D7_RNAseq

tag: genotype/variation


title: exp2-OTS514 LEN CFZ

value: OTS514 LEN CFZ


title: Zfc3h1_KO_1_ESC_SUZ12_RIPseq


title: Zfc3h1_KO_2_EB_D7_RNAseq


title: exp3-CFZ

value: CFZ


title: WT_2_EB_D7_RNAseq


title: Post-4

city: Houston

first: Sreyashi

last: Basu

address: 7455 Fannin Street

institute: MDACC

description:
2052-Post
FFPE

hyb_protocol: Digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. 300ng of each RNA sample was added to the CodeSet in hybridization buffer and incubated at 65¬∞C for 16 hours. 12 samples were processed per cartridge. Each cartridge was subjected to a 3 hour automated processing  on the Prep Station

scan_protocol: Data Collection was carried out in theGEN2 nCounterTM Digital Analyzer. Digital images were processed and the barcode counts are tabulated in a comma separated value (CSV) format. Raw target counts were collected using the NanoString data collection software, nSolver.

data_processing: Six positive control probes (POS A-F) and their corresponding RNA targets at various concentrations from 128 fM to 0.5 fM were included in the assay to account for systematic variation introduced by pipetting, sample purification, and imaging. Negative control probes (with no corresponding targets, NEG A-H) were included to control for non-specific background noise, i.e. non-specific carryover of reporter probes. The raw target counts were background corrected, normalized to the mean of the positive control probes for each assay, and then normalized to the geometric mean of the reference genes (B2M, PGK1, and RPLP0). nSolver computes a normalization factor for each assay based on the average of positive control counts for the whole data set. NanoString recommends that for optimal results positive control normalization factors range between 0.3 and 3.0 for all assays.

source_name: anti-PD-1 treated patient_primary GBM

extract_protocol: On average, 5 um-thick FFPE sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a immunopathologist (JB)

tag: subject group

value: anti-PD-1 treated patient

value: primary GBM


title: Post-3

description:
2045-Post
FFPE


title: exp2-CFZ


title: WT_1_EB_D7_RNAseq

value: Wildtype


title: WT_1_ESC_EZH2_RIPseq


title: Post-2

description:
1849-Post
FFPE


title: 12hr_5ng

value: 6 nM TrtE


title: 8hr_DMSO

value: 8 hours


title: Post-1

description:
1590-Post
FFPE


title: WT_2_ESC_SUZ12_RIPseq

value: Embryonic stem cells


title: Pre-6

description:
2727-Pre
FFPE

source_name: untreated patient_primary GBM

value: untreated patient


title: 8hr_20ng


title: WT_1_ESC_SUZ12_RIPseq


title: WT_2_ESC_EZH2_RIPseq


title: 8hr_5ng


title: Zfc3h1_KO_2_ESC_RIPseq_input


title: Zfc3h1_KO_1_ESC_RIPseq_input


title: Pre-4

description:
2298-Pre
FFPE


title: 4hr_DMSO

value: 4 hours


title: 4hr_20ng


title: Pre-3

description:
2266-Pre
FFPE


title: WT_2_ESC_RIPseq_input


title: WT_1_ESC_RIPseq_input


title: PAX7neg-A_rep2: Donor A - PAX7 negative myoblast population

status: Public on Nov 11 2019

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Single-cell sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants. The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
processed data files format and content: Digital Gene Expression matrices contain UMI counts per cell and per gene
Genome_build: GRCh38

source_name: Human Primary Myoblasts

growth_protocol: Muscle biopsy specimens for myoblast isolation were obtained from M. vast. lat. after IRB approval (EA1/203/08 and EA2/051/10). Myoblast isolation was performed as described. (Marg et al., 2012) Contamination of myoblast cultures with fibroblasts was always below 5%. Myoblasts were seeded and grown in skeletal muscle growth medium (ProVitro, Germany) until they reached 50-60% confluence.

extract_protocol:
Not applicable
Drop-seq (Alles et al BMC Biol 15; adapted from Macosko et al 2015 Cell 161)

value: human primary myoblasts cell line

tag: passage number

tag: type of muscle

value: M vast lat

tag: donor age (yrs)

tag: gender

value: female

tag: pax7 positive myoblasts

tag: method

value: Single-cell mRNA Seq


title: PAX7neg-C: Donor C - PAX7 negative myoblast population

tag: cell type

value: male


title: PAX7pos-H_rep2: Donor H - PAX7 positive myoblast population


title: PAX7neg-H: Donor H - PAX7 negative myoblast population


title: PAX7neg-H_rep2: Donor H - PAX7 negative myoblast population


title: PAX7null: Patient with homozygous PAX7 splicing mutation and PAX7 deficient myoblasts

value: Splicing mutation in Intron 1


title: PAX7pos-H: Donor H - PAX7 positive myoblast population


title: PAX7pos-G: Donor G - PAX7 positive myoblast population


title: PAX7neg-A: Donor A - PAX7 negative myoblast population


title: PAX7pos-A_rep2: Donor A - PAX7 positive myoblast population


title: PAX7pos-A: Donor A - PAX7 positive myoblast population


title: Pre-5

description:
2305-Pre
FFPE

tag: tissue


title: PAX7pos-C: Donor C - PAX7 positive myoblast population


title: UCS2 control Rep 3

city: Dallas

first: Ileana

middle: C

last: Cuevas

state: TX

address: 5323 Harry hines Blvd. NB6.112

department: Pathology

institute: University of Texas Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v1.127)
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: Fbxw7-/-; Pten-/- uterine carcisnosarcoma cells

growth_protocol: UCS1 and UCS2 cells were grown in DMEM +10% FBS in the presence of doxycycline 500ng/ml

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen #74104). RNA was treated with RNAse-free DNAse (Qiagen #79254) and Qubit quantified for library preparation
4 ug of total DNAse-treated RNA was prepared with TruSeq Stranded Total RNA LT Sample Prep kit (Illumina). Poly-A-RNA was purified and fragmented before strand specific cDNA synthesis. cDNA was poly A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples were quantified by Qubit before normalization and pooling. Samples were sequenced on the Illumina NextSeq 500 with read configuration as 75 bp, single end reads. 25-40 million reads were generated per sample.

treatment_protocol: UCS1 and UCS2 cells were transduced with A) lentivirus expressing Fbxw7 under a Tet inducible promoter (FBXW7) or B) lentivirus with vector only (PLVX) AND c) with lentivirus expressing TetON. Cells were selected with puromycin (pLVX) and G418 (tetON).

value: endometrial carcinosarcoma

tag: genotype

value: Fbxw7-/-; Pten-/-

value: Cells stably expressing pLVX and TetON vector


title: UCS2 control Rep 2


title: 4hr_5ng

value: human foreskin fibroblast cells (HFF)

value: intracellular tachyzoites


title: Fbxw7 overexpressing UCS1 Rep 3

value: Cells stably expressing pLVX-Fbxw7 and TetON vector


title: Fbxw7 overexpressing UCS1 Rep 2


title: UCS2 control Rep 1


title: UCS1 control Rep 3


title: Pre-2

description:
2007-Pre
FFPE

value: primary GBM


title: Fbxw7 overexpressing UCS1 Rep 1


title: UCS1 control Rep 2


title: Fbxw7 overexpressing UCS2 Rep 3


title: UCS1 control Rep 1


title: Fbxw7 overexpressing UCS2 Rep 2


title: PAX7neg-G: Donor G - PAX7 negative myoblast population


title: Fbxw7 overexpressing UCS2 Rep 1


title: D15-WT-GC-Bcell_Rep2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
The D10 libraries were mapped to the GRCm38/mm10 genome by using Subread-1.6.0; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in 3 libraries. Counts were converted to log2 counts per kilobase per million(log2 FKPM), quantile normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.15 or less.
The libraries were merged by their types and dates, ending up with 4 merged libraries: D10-TbetKO, D10-WT, D15-TbetKO and D15-WT. The merged libraries were then mapped to the GRCm38/mm10 genome by Subjunc in the Subread package, and SNPs were called from the mapping results by exactSNP in the Subread package. The SNPs were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1), and only SNPs assigned to the exon regions in the IghV genes were used in the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each D10 library. The supplementary file, Supp-Count-Table.txt, includes raw read counts for genes in the D10 libraries.

source_name: Germinal center B cell (CD19+ CD138- GL7+ CD38low), wild-type

extract_protocol:
RNA purification was performed following the manufacturer's protocol using the RNAeasy Plus Mini Kit (Qiagen).
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

treatment_protocol: Cells were isolated from the spleens of P. berghei ANKA-infected mice at day 10 and 15 post-infection by flow cytometry sorting

tag: strain

value: CD23cre T/+

value: Spleen

value: WT GC Bcells

tag: infection

value: P. berghei ANKA


title: D15-WT-GC-Bcell_Rep3


title: Pre-1

description:
1814-Pre
FFPE

value: untreated patient


title: D15-WT-GC-Bcell_Rep1


title: D15-TbetKO-GC-Bcell_Rep2

source_name: Germinal center B cell (CD19+ CD138- GL7+ CD38low), T-bet-deficient

value: Tbx21 fl/fl CD23cre T/+

value: TbetKO GC Bcells


title: D15-TbetKO-GC-Bcell_Rep3


title: D15-TbetKO-GC-Bcell_Rep1


title: D10-TbetKO-GC-Bcell_Rep1


title: D10-WT-GC-Bcell_Rep3


title: D10-WT-GC-Bcell_Rep2


title: WT-5241-CXCR3plus-GC-B_Rep2

data_processing:
The paired-end libraries were mapped to the GRCm38/mm10 reference genome by using Subread-1.6.0. Only uniquely mapped read-pairs were allowed in mapping. Peaks were then called from the mapping results by using Homer (v4.7) at an FDR cutoff of 1E-6.
The peaks from all the samples were merged by taking the unions of the peaks; the merged peaks were then assigned to the nearest genes in the NCBI RefSeq gene annotation for mm10 (build 38.1). The mapped read-pairs were assigned to the merged peak regions by using featureCounts.
Merged peaks were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 5 in any library. Counts were converted to log2 CPM values, quantile normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each merged peak, and empirical Bayes moderated t-statistics were used to assess differences of accessibility of the chromatin. Merged peaks were called differential if they achieved a false discovery rate of 0.1 or less, and have a fold change greater than 2 between the two compared cell types.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts and TAB-delimited log2 CPM

source_name: Germinal center B cell (CD4- CD19+ CD138- GL7+ CD38low CXCR3+), wild-type

extract_protocol:
DNA was extracted using cell lysis buffer as described previously (Buenrostro, et al 2013)
Libraries were generated following the protocol as described previously (Buenrostro, et al 2013)

value: WT CXCR3 + GC Bcells


title: D10-WT-GC-Bcell_Rep1


title: bsuq flg3

city: Stanford

first: Chan Ho

last: Park

state: CA

address: 260 Panama street

institute: Carnegie institution for science

data_processing:
alignment- TopHat2 in iPlant
Quantitative comparison- Cuffmerge, Cufflinks and Cuffdiff in iPlant
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: 3 days dark and 12 days light grown seedling

growth_protocol: WT and bsu-q seeds were germinated in the dark for 3 days, seedlings with weak phenotype (long hypocotyl) were removed from the bsu-q samples, and then the plants were grown under light for 12 days.

extract_protocol:
Total RNA was extracted from the wild-type and bsu-q seedlings treated with flg22 or mock solution using the Spectrum Plant Total RNA kit (Sigma).
cDNA libraries were constructed using a TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s instruction.

treatment_protocol: Seedlings on plates were submerged in 1 μM flg22 or mock solution for 1 min. After decanting the solution, the seedlings were then incubated in growth chamber for 1 hr.

tag: ecotype

value: seedling

value: bsu-q


title: bsuq flg2

tag: treatment


title: WT-5241-CXCR3plus-GC-B_Rep1


title: bsuq flg1


title: TbetKO-5235-GC-B_Rep1

source_name: Germinal center B cell (CD4- CD19+ CD138- GL7+ CD38low), T-bet-deficient


title: Col-0 flg3

value: wild type


title: Col-0 flg1


title: D10-TbetKO-GC-Bcell_Rep2


title: bsuq ct3

value: untreated


title: D10-TbetKO-GC-Bcell_Rep3


title: bsuq ct1


title: CD6

first: Zintis

last: Inde

address: 327 Campus Drive

institute: Stanford University

data_processing:
Reads with adaptor contamination, >10% uncertain nucleotides, or >50% nucleotides with base quality <20 were filtered out
Filtered reads were aligned to the reference genome using Tophat 2.0.12
Genome_build: hg19
Supplementary_files_format_and_content: CSV files contain fpkm values for each sample

source_name: Non-Small Cell Cancer Cell Line

growth_protocol: Cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
RNA was extracted using Qiashredder and Rneasy Plus Mini Kits
Library prep was conducted by Novogene (Sacramento, CA) using standard Illumina protocols

treatment_protocol: Cells were treated for 96 hours with the indicated drug or DMSO vehicle control

tag: cell line

value: DMSO

tag: pimasertib dose


title: CD4


title: AH2

value: Pimasertib

value: 5 microM


title: AH4


title: Col-0 ct3


title: Col-0 ct1


title: WUS-GR TSA RNA-Seq3

city: Heidelberg

first: Jan

middle: U

last: Lohmann

address: Im Neuenheimer Feld 230

department: Stem Cell Biology

institute: Centre for Organismal Studies

description: RNA-Seq treatment

data_processing:
Quality control: FastQC
Raw sequence concatenation
Read alignment: HISAT2
Read counting: featureCounts
DEG calling: DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: raw count matrix in .txt format

source_name: whole seedling

growth_protocol: 23°C; 65% humidity;  16h light/8h dark; LED lights 200µE

extract_protocol:
RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg input was used.

treatment_protocol: 0.015% Silwet, 25µM dexamethasone, with or without  1µM trichostatin, in 0.5xMS for 2h

tag: developmental stage

value: 5 days after germination

tag: genotype/variation

value: 2h 25uM dexamethasone,1uM trichostatin


title: CP6


title: Col-0 TSA RNA-Seq3

description: RNA-Seq control


title: Col-0 TSA RNA-Seq2

description: RNA-Seq control


title: bsuq ct2


title: WUS-GR TSA RNA-Seq2

description: RNA-Seq treatment


title: exp2-LEN

source_name: H929 cells

value: LEN

tag: replicate


title: AL4


title: Col-0 flg2


title: AL2


title: CP4


title: Col-0 TSA RNA-Seq1

description: RNA-Seq control


title: WUS-GR TSA RNA-Seq1

description: RNA-Seq treatment


title: AD4


title: Col-0 RNA-Seq3

description: RNA-Seq control

value: 2h 25uM dexamethasone


title: CD8_thymus_5

city: OSLO

first: Benedicte

middle: Alexandra

last: Lie

address: Kirkeveien 166, Laboratoriebygget

department: Department of Medical Genetics

country: Norway

institute: OUS

description: In compliance with the Norwegian Health Research Act and the Norwegian Data Protection Act, we are unfortunately not permitted to deposit the raw transcriptome data from this study.

data_processing:
Low quality reads and adapter sequence was trimmed with Trimmomatic v0.33
Reads were mapped with TopHat2 v2.1.0 to genome ( EnsemblGRCh38) and transcriptome reference (Ensembl release 80)
Features were summarised by FeatureCounts (subread v1.4.6-p3), at gene level
Normalisation and differential gene expression analysis carried out in edgeR (v3.16.5)
Genome_build: EnsemblGRCh38
Supplementary_files_format_and_content: Raw counts in csv format
Supplementary_files_format_and_content: TMM normalised FPKM in csv format

source_name: thymus

extract_protocol:
Thymic tissue (~10 g) was collected and trated with collagenase D (Roche Life Science, Basel, Switzerland) and Liberase TM (Roche Life Science) untill completely dissolved. Desired cell populations were sorted manually by targeted magnetic beads (STEMCELL Technologies, Vancouver, Canada).
The CD4+ T cells from thymus and blood were isolated with EasySep™ Human CD4+CD25+ T Cell Isolation Kit. The blood CD8+ T cells were isolated using EasySep™ Positive CD8+ Selection Kit (STEMCELL Technologies), while the thymic CD8+ T cells were isolated by negative selection using the human CD8+ T cell enrichment kit (STEMCELL Technologies).
total RNA was extracted by RNeasy Plus mini Kit (Qiagen)
The cDNA libraries were prepared using Truseq Stranded Total RNA Kit with Ribo-Zero GOLD set A (Illumina, California, USA # RS-122-2301), using standard Illumina protocols, and sequenced on Illumina HiSeq2000 or 2500, paired end.

value: CD8+ T cells

value: thymus

tag: sample type

value: individual sample

tag: age

value: infant


title: WUS-GR RNA-Seq3

description: RNA-Seq treatment


title: CD8_thymus_4


title: CD8_thymus_3


title: Col-0 RNA-Seq2

description: RNA-Seq control


title: CD8_thymus_2


title: CD8_thymus_1


title: CD4_bloodadult

source_name: peripheral blood

value: CD4+ T cells

value: blood

value: pooled samples

value: adult


title: WUS-GR RNA-Seq2

description: RNA-Seq treatment


title: CD4_bloodinfant_4


title: WUS-GR RNA-Seq1

description: RNA-Seq treatment


title: CD4_bloodinfant_3


title: CD4_bloodinfant_2


title: CD4_bloodinfant_1


title: Col-0 RNA-Seq1

description: RNA-Seq control


title: AD2


title: Col-0 Methylation

description: H3K27me ChIP-Seq control

data_processing:
Quality control: FastQC
Raw sequence concatenation of same conditions
Read alignment: BWA
Peak-calling: hiddenDomains
Peak annotation: PAVIS
Genome_build: TAIR10
Supplementary_files_format_and_content: BED file

extract_protocol:
ChIP assays were performed from 3 g of fresh weight each as previously described (Gendrel et al., 2005, and Pfeiffer et al., 2016) with modifications to tissue fixation and nuclei preparation. Plant material was fixed in 100mM sodium phosphate buffer, pH 7.0, 50mM NaCl, 100mM sucrose, and 0.33% formaldehyde for three times 10 min under vacuum. Nuclear extracts were prepared according to the INTACT protocol (Deal and Henikoff, 2011) and chromatin sheared according to Fan et al. (2008). Cleared nuclear extracts were split in two and incubated each with 20 μl of RFP-Trap_A (ChromoTek) for 4 h over night for immunoprecipitation. MinElute Reaction Cleanup Kit columns (Qiagen) were used for purification of the DNA fragments. Enrichment of specific DNA fragments was validated by qPCR at the ARR7 promoter region (Leibfried et al., 2005) by comparing immunoprecipitated DNA of WUS-GR and control samples.
Two independent sequencing libraries were generated for the using pooled DNA from 9 individual ChIP preparations. Libraries were prepared for Illumina Sequencing using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240) with the NEBNext Multiplex Oligos for Illumina (E7335 and E7500). Libraries were quantified using the Qubit Fluorometer from Invitrogen, and their size determined using the DNA 1000 Assay on the BioAnalyzer. Sequencing was performed on the Illumina HiSeq 2000 Instrument 50 base SE (plus index read).

treatment_protocol: 0.015% Silwet, with or without 25µM dexamethasone, in 0.5xMS for 2h

tag: antibody

value: anti H3K27me3 (07-449; Merck Millipore)

value: 2h 25 uM dexamethasone


title: WUS-GR Methylation

description: H3K27me ChIP-Seq treatment


title: CD4_thymus_3


title: Col-0 Acetylation

description: H3K9ac ChIP-Seq control

value: anti H3ac (K9;K14) (06-599; Merck Millipore)


title: WUS-GR Acetylation

description: H3K9ac ChIP-Seq treatment


title: CD4_thymus_4


title: CD4_thymus_2


title: Col-0 ChIP-Seq

description: ChIP-Seq control

value: RFP-trap (rta-100; ChromoTek)


title: WUS-GR ChIP-Seq

description: ChIP-Seq treatment


title: CD4_thymus_1


title: UMUC9_r2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description:
UMUC9 replicate 2
bru-labeled RNA

data_processing:
Library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3)
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Uniquely mapped reads were counted in 1kb genomic bins and bin RPKM values calculated as previously described (Paulsen et. al. 2013)
Genome_build: hg38
Supplementary_files_format_and_content: Please refer to Table S1 (Supplemntary Info) for information on cell lines. The columns of the txn_units.bed indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) length of txn unit  (7) read count (8) RPKM

growth_protocol: BxPC3, UML49, UM5, GM12878, GM12891, HCT116 were grown in RPMI (RPMI 1640, 10% FBS, 100 U/ml penicillin, 100 U/ml streptomycin). A2058, HEK293, A375, A673, MiaPaCa, panc1, U2OS, UM16, UM28 and UM59 were grown in DMEM (DMEM, 10% FBS, 100 U/ml penicillin, 100 U/ml streptomycin) and MEM growth media (Minimal Essential Medium, 10% FBS, 1x MEM Amino Acids, 1x Non-Essential Amino Acids, 2 mM l-glutamine, 1X antibiotic–antimycotic, 1x MEM vitamin mixture, 0.15% (w/v) sodium bicarbonate) was used for HEPB3, HepG2, MCF7, U87, UMUC9 and human fibroblasts HF, CSB and XPC. HPDE were grown in keratinocyte serum-free medium (Invitrogen Life Technologies, Inc., Carlsbad, CA) supplemented with 50 μg/mL bovine pituitary extract (Invitrogen) and 5.0 ng/mL recombinant human EGF (Invitrogen); HPNE were grown in three volumes of DMEM and one volume of medium M3, with the mixture supplemented with 5% fetal calf serum and 10 ng/mL EGF; HAP1 and K562 were grown in IMDM with 10% FBS and antibiotics; SHEP1 in 1:1 mix of MEM and F12 media with 10% FBS. iPSCs were reprogrammed from HF (32). Typically, 4 x 106 cells were harvested per sample in 2-3 10cm plates (~80% confluency), yielding ~80-100 mg of total RNA.

extract_protocol:
For bruseq and BruUV-seq, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruseq

tag: time between end of bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: UML49

description: bru-labeled RNA


title: UM59

description: bru-labeled RNA


title: UMUC9_r1

description:
UMUC9 replicate 1
bru-labeled RNA


title: UM59_UV

description: bru-labeled RNA

value: BruUV-seq


title: UM5_r1

description:
UM5 replicate 1
bru-labeled RNA


title: UM5_UV

description: bru-labeled RNA


title: UM28_UV

description: bru-labeled RNA


title: Donor-blunt Acceptor-N

city: Austin

first: Alan

last: Lambowitz

address: 2500 Speedway

institute: University of Texas at Austin

description: synthetic oligonucleotide

data_processing:
Library strategy: TGIRT-seq
reads from each dataset were trimmed from the 5’ end using Cutadapt v2.5 to re-move all but the last 3 nucleotides of the 5’ acceptor (GAC) by using the following pa-rameters: cutadapt -O 10 --nextseq-trim=20  --trim-n -q 20 --discard-untrimmed -g CGCCGGACCGTGCACCATCTGGAGTTATAGAGATGAGTCTCACATA -j 8 -e 0.1 -o {Step1 trimmed reads} {Read 1 file}
reads were then trimmed from the 3’ end to leave the junction sequences flanked by GAC at the 5’ end and CGC (acceptor) or AGA (donor) at the  3’ end by using the following parameters: cutadapt -O 10 --nextseq-trim=20  --trim-n -q 20 --discard-untrimmed -a CGGACCGTGCACCAT -a TCGGAAGAGCACACG -j 8 -e 0.1 -o {Step2 trimmed reads} {Step1 trimmed reads}
trimmed reads containing either acceptor-donor junction 5’-GAC-(N)n-AGA-3’ or ac-ceptor- acceptor junction 5’-GAC-(N)n-CGC-3’ were then binned and counted
Genome_build: N/A
Supplementary_files_format_and_content: count of junction reads

organism: synthetic construct

source_name: Integrated DNA technologies

extract_protocol:
N/A; synthetic oligonucleotdes
RNA sequencing libraries were prepared by using TGIRT-III (InGex), a commercial version of GsI-IIC RT, with different R2 RNA/R2R starter duplexes and acceptor nucleic acids as indicated in the text. The initial template template-switching reactions for addition of the R2R adapter to the 5' end of the cDNA were done as described above with 500 nM TGIRT-III enzyme, 50 nM unlabeled starter duplex, and 100 nM acceptor RNA for 15 min at 60 °C. After terminating the reactions with NaOH and neutralization with HCl as described above for template-switching reactions, the volume was raised to 100 μl with H2O, and cDNA products containing the R2R adapter attached to their 5' end were cleaned-up by using a MinElute column (Qiagen) to remove unused primer. A 5’ adenylated R1R adapter was then ligated to the 3' end of the cDNA using Thermostable 5’ AppDNA/RNA ligase (New England Biolabs) for 1 h at 65 °C. After another MinElute clean up, the entirety of the eluent was used for a 12 cycle PCR reaction using Phusion polymerase (ThermoFisher), and the resulting libraries were cleaned up by using 1.4x Ampure XP beads to remove residual primers, primer dimers, salts, and enzymes. The quality of the libraries was assessed by using a 2100 Bioanalzyer Instrument (Agilent) with a High Sensitivity DNA chip (Agilent). The libraries were sequenced on an Illumina NextSeq instrument to obtain 1-2 million 75-nt paired-end reads. Read 1 was used for analysis.

tag: starter molecule

value: blunt end R2 RNA/ R2R DNA duplex

tag: acceptor

value: 50 nt RNA oligonucleotide with 3' equimolar N


title: UM5_r2

description:
UM5 replicate 2
bru-labeled RNA


title: UM28

description: bru-labeled RNA


title: xpc

description: bru-labeled RNA

source_name: xpc


title: UM16

description: bru-labeled RNA


title: Donor-overhang-G Acceptor-C

description: synthetic oligonucleotide

value: 3' G DNA primer - overhang  R2 RNA/ R2R DNA duplex

value: 50 nt RNA oligonucleotide with 3' C


title: U87_r2

description:
U87 replicate 2
bru-labeled RNA


title: Matched: donor-overhang-G Acceptor-C

description: synthetic oligonucleotide


title: Donor-overhang-C Acceptor-G

description: synthetic oligonucleotide

value: 3' C DNA primer - overhang  R2 RNA/ R2R DNA duplex

value: 50 nt RNA oligonucleotide with 3' G


title: C-Myc-sh, biological rep3

city: Wuhan

first: Ming

last: Yue

address: Hangkong Road 13, Qiaokou District

institute: Tongji Medical College, Huazhong University of Science and Technology

description:
C-Myc-sh_3
Gene expression data from Daudi cells transfected with C-Myc shRNA.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, GeneSpring Software12.6.1 (Agilent Technologies, Santa Clara, CA, US).

source_name: Daudi cell line, C-Myc shRNA

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin-labeled cRNA.

growth_protocol: Daudi cells were maintained in RPMI media (GIBCO) containing 10% FBS (GEMENI), 2 mM L-glutamine and 1x penicillin/streptomycin in a 5% CO2 incubator (ESCO).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Daudi cells were infected with control shRNA, Slc7a5 shRNA or C-Myc shRNA, respectively, and selected with puromycin for 48 hours.

value: Daudi

tag: shRNA

value: C-Myc


title: Donor-overhang-A Acceptor-U

description: synthetic oligonucleotide

value: 3' A DNA primer - overhang  R2 RNA/ R2R DNA duplex

value: 50 nt RNA oligonucleotide with 3' U


title: C-Myc-sh, biological rep1

description:
C-Myc-sh_1
Gene expression data from Daudi cells transfected with C-Myc shRNA.


title: C-Myc-sh, biological rep2

description:
C-Myc-sh_2
Gene expression data from Daudi cells transfected with C-Myc shRNA.


title: Slc7a5-sh, biological rep1

description:
Slc7a5-sh_1
Gene expression data from Daudi cells transfected with Slc7a5 shRNA.

source_name: Daudi cell line, Slc7a5 shRNA


title: U2OS_r3

description:
U2OS replicate 3
bru-labeled RNA


title: Slc7a5-sh, biological rep3

description:
Slc7a5-sh_3
Gene expression data from Daudi cells transfected with Slc7a5 shRNA.


title: Ctrl-sh, biological rep2

description:
Ctrl-sh_2
Gene expression data from Daudi cells transfected with control shRNA.

source_name: Daudi cell line, control shRNA

value: control


title: Donor-overhang-T Acceptor-A

description: synthetic oligonucleotide

value: 3' T DNA primer - overhang  R2 RNA/ R2R DNA duplex

value: 50 nt RNA oligonucleotide with 3' A


title: Ctrl-sh, biological rep3

description:
Ctrl-sh_3
Gene expression data from Daudi cells transfected with control shRNA.


title: Ctrl-sh, biological rep1

description:
Ctrl-sh_1
Gene expression data from Daudi cells transfected with control shRNA.


title: Slc7a5-sh, biological rep2

description:
Slc7a5-sh_2
Gene expression data from Daudi cells transfected with Slc7a5 shRNA.


title: Mismatched: donor-overhang-C Acceptor-C

description: synthetic oligonucleotide


title: Donor-blunt Acceptor-C

description: synthetic oligonucleotide


title: UM16_UV

description: bru-labeled RNA

value: 0.5 hours


title: U2OS_r2

description:
U2OS replicate 2
bru-labeled RNA

value: bruseq

value: 0 hours


title: U2OS_r1

description:
U2OS replicate 1
bru-labeled RNA

value: Bromouridine (Bru)


title: Donor-blunt Acceptor-G

description: synthetic oligonucleotide

value: blunt end R2 RNA/ R2R DNA duplex


title: U87_r1

description:
U87 replicate 1
bru-labeled RNA


title: T47D_r1

description:
T47D replicate 1
bru-labeled RNA


title: Donor-blunt Acceptor-A

description: synthetic oligonucleotide


title: T47D_r2

description:
T47D replicate 2
bru-labeled RNA


title: panc1_r3

description:
panc1 replicate 3
bru-labeled RNA


title: CD8_bloodadult

tag: cell type

value: CD8+ T cells

tag: tissue

value: blood

value: pooled samples

value: adult


title: CD8_bloodinfant_3

value: individual sample

value: infant


title: CD8_bloodinfant_1


title: Donor-blunt Acceptor-U

description: synthetic oligonucleotide


title: panc1_UV

description: bru-labeled RNA

value: BruUV-seq


title: panc1_r4

description:
panc1 replicate 4
bru-labeled RNA


title: panc1_r1

description:
panc1 replicate 1
bru-labeled RNA


title: panc1_r2

description:
panc1 replicate 2
bru-labeled RNA


title: panc1_r5

description:
panc1 replicate 5
bru-labeled RNA


title: AGGRESSIVE CLL [VB1664]

city: Columbus

first: Carlo

middle: Maria

last: Croce

state: OHIO

address: 460 West 12TH Avenue

department: Cancer Biology & Genetics

institute: The Ohio State University

description:
VB1664
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

data_processing:
Raw sequenced reads were pre-processed by trimming the QIAseq 3’ adapter (AACTGTAGGCACCATCAAT) as well as the 3’ universal Illumina adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) via the tool Cutadapt (https://cutadapt.readthedocs.org/) (parameters: min length=12, max length=50, min_quality=25, -n 1 -O 5 --match-read-wildcards), and finally quality-filtered via tool ConDeTri (PMID: 22039460) (parameters: -pb=fq -lq=20 -hq=30 -minlen=15 -sc=33).
For tsRNA detection, pre-processed fastq files were then analyzed by leveraging a modified version of the tRNA fragments detection tool tDRmapper (PMID: 26530785), allowing exclusively for the exact mapping of filtered sequencing reads on a customized version of the tRNA genomic space.
After mapping, in-house scripts were employed to parse tDRmapper output files, (.mapped files), to collect and collapse raw counts which mapped to locations within pre-tRNA molecules contained in the provided tRNA space and which were annotated to be tsRNA loci, by leveraging a custom annotation file associating tsRNA IDs, their location and length, with pre-tRNA IDs as reported in the custom tRNA space. Raw counts for all tsRNA molecules which were detected having SNPs were all combined, along with their reference tsRNA sequence count when detected, into a single collapsed read count per sample.
For tRF detection, pre-processed fastq files were analyzed by leveraging the recently published tool MINTmap (PMID: 28220888), applied with standard parameters, and extracted raw counts were collapsed through in-house scripts.
A minimum expression filtering was applied on raw counts prior to normalization, with detected molecules retained if they reported at least 5 raw reads in each of at least 8 samples. As recommended (PMID: 20196867), filtered molecules were normalized by applying the TMM method (trimmed mean of M-values) and statistical analysis of the data was carried out.
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: Txt files contain the expression (normalized counts) of detected tsRNAs and tRFs which survived minimum expression threshold in each sample.

source_name: CD5+/CD19+ B cells

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher) following the standard protocol.
After extraction, 2 µg of total RNA for each sample were analyzed for quality control on the Agilent 2100 Bioanalyzer. Universal cDNA synthesis, cDNA cleanup, library amplification and library cleanup were performed using the QIAseq™ miRNA Library Kit (Qiagen) according to the manufacturer`s protocol.
Sequencing libraries were generated on Illumina® HiSeq 2500 in Rapid Mode Fast Flow cell (50 bp single-end reads were generated).

value: CD5+/CD19+ B cells

tag: diagnosis

value: Chronic lymphocytic leukemia

tag: course

value: AGGRESSIVE CLL

tag: vh% homology

tag: FISH or karyotype homology


title: AGGRESSIVE CLL [VB1243]

description:
VB1243
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: AGGRESSIVE CLL [VB1658]

description:
VB1658
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

value: Trisomy 12


title: MiaPaCa_r4

description:
MiaPaCa replicate 4
bru-labeled RNA

source_name: MiaPaCa


title: MiaPaCa_r6

description:
MiaPaCa replicate 6
bru-labeled RNA


title: CD8_bloodinfant_2


title: AGGRESSIVE CLL [VB1493]

description:
VB1493
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: MiaPaCa_r3

description:
MiaPaCa replicate 3
bru-labeled RNA


title: AGGRESSIVE CLL [VB1650]

description:
VB1650
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

value: Normal Karyotype


title: MiaPaCa_r5

description:
MiaPaCa replicate 5
bru-labeled RNA

value: 0.5 hours


title: AGGRESSIVE CLL [VB1653]

description:
VB1653
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: MiaPaCa_r2

description:
MiaPaCa replicate 2
bru-labeled RNA

value: bruseq


title: AGGRESSIVE CLL [VB1492]

description:
VB1492
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: AGGRESSIVE CLL [VB1647]

description:
VB1647
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: AGGRESSIVE CLL [VB1488]

description:
VB1488
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: MiaPaCa_r1

description:
MiaPaCa replicate 1
bru-labeled RNA

value: 0 hours


title: AGGRESSIVE CLL [VB1485]

description:
VB1485
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: MCF7_r5

description:
MCF7 replicate 5
bru-labeled RNA

value: Bromouridine (Bru)


title: MCF7_r3

description:
MCF7 replicate 3
bru-labeled RNA


title: INDOLENT CLL [VB1212]

description:
VB1212
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

value: INDOLENT CLL


title: INDOLENT CLL [VB1477]

description:
VB1477
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: MCF7_r2

description:
MCF7 replicate 2
bru-labeled RNA


title: MiaPaCa_UV

description: bru-labeled RNA


title: MCF7_r1

description:
MCF7 replicate 1
bru-labeled RNA


title: INDOLENT CLL [VB1474]

description:
VB1474
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: INDOLENT CLL [VB1473]

description:
VB1473
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: K562_UV

description: bru-labeled RNA


title: INDOLENT CLL [VB1472]

description:
VB1472
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: K562_r5

description:
K562 replicate 5
bru-labeled RNA


title: K562_r4

description:
K562 replicate 4
bru-labeled RNA


title: INDOLENT CLL [VB1469]

description:
VB1469
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: CTRL [VB6141]

description:
VB6141
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

source_name: Normal CD19+ B-cells

value: CD19+ B-cells

value: Healthy

value: HEALTHY


title: HPNE

description: bru-labeled RNA

source_name: HPNE


title: MCF7_r4

description:
MCF7 replicate 4
bru-labeled RNA


title: INDOLENT CLL [VB1465]

description:
VB1465
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: K562_r1

description:
K562 replicate 1
bru-labeled RNA


title: INDOLENT CLL [VB1468]

description:
VB1468
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: K562_r2

description:
K562 replicate 2
bru-labeled RNA


title: CTRL [VB6139]

description:
VB6139
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: INDOLENT CLL [VB1470]

description:
VB1470
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

value: UNKNOWN


title: HPDE_UV

description: bru-labeled RNA


title: CTRL [VB6140]

description:
VB6140
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: CTRL [VB6138]

description:
VB6138
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: HPNE_UV

description: bru-labeled RNA


title: CTRL [VB6134]

description:
VB6134
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: CTRL [VB6136]

description:
VB6136
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: HME

description: bru-labeled RNA

source_name: HME


title: HF_r4

description:
HF replicate 4
bru-labeled RNA

source_name: HF


title: HF_r3

description:
HF replicate 3
bru-labeled RNA


title: CTRL [VB6133]

description:
VB6133
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt


title: HPDE

description: bru-labeled RNA

source_name: HPDE


title: K562_r3

description:
K562 replicate 3
bru-labeled RNA


title: HEPG2

description: bru-labeled RNA


title: FS56

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description:
FER021
fertility.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: Sperm

growth_protocol:
A single center (Urology Department at Hospital Universitari i Politècnic La Fe), prospective and open clinical study. The IRB approval code protocol 2015-002521-19. We included two groups (infertility vs fertility). The infertility men (inability of the couple to become pregnant after one year of sexual activity), included caucasians between 25-45 years of age with a total sperm concentration (concentration in millions/mL x volume in mL) between 1-10 million (oligozoospermia) in at least 2 spermiograms obtained after a 2-4 day period of sexual abstinence and with a 7-day separation period between tests. The hormone profile used inclusion criteria of FSH 2-12 IU/mL, total testosterone >300 ng/mL and bioavailable testosterone (calculated with the Sexual Hormone Binding Globulin or SHBG albumin) >145 ng/dL. The fertile control group included caucasians without vasectomy and had a child in the last five years with a sperm concentration and motility above the 50th percentile according
to the parameters set forth in the 5th edition of the World Health Organization (WHO) guidelines in at least two spermiograms obtained after a 2-4 day period of sexual abstinence and with a 7-day period between tests. The hormones profiled used inclusion criteria of estradiol <50 pg/mL, FSH <4.5 IU/L, total testosterone >300 ng/dL and bioavailable testosterone >145
ng/dL.

extract_protocol:
Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual sperm DNA samples were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with a the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 minutes and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4 C. After the incubation the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 minutes and the supernatant was discarded, then washed with 1xIP buffer 3 times. The washed bead-DNA solution was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55 C and then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20min at 4˚C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min. then centrifuged again at 14,000rpm for 5min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212)
The MeDIP DNA samples were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: The infertility group received 150 IU of urinary or recombinant FSH three times per week for 12 weeks and the fertile control group did not received treatment. After three months of treatment, semen analysis and hormone profiles were retested in both groups. A validation set of samples collected that were selection failures due to a variety of reasons and not used in the infertility DMR analysis for DMR identification.

tag: fertility

value: fertile

tag: treatment response

tag: selection failure

value: no


title: HF_r2

description:
HF replicate 2
bru-labeled RNA


title: HEPB3

description: bru-labeled RNA


title: FS55

description:
FERUNCODED3
sf.results.csv.gz

value: yes


title: FS52

description:
INFUNCODED1
sf.results.csv.gz

value: infertile


title: FS54

description:
FERUNCODED2
sf.results.csv.gz


title: HCT116_r4

description:
HCT116 replicate 4
bru-labeled RNA


title: FS51

description:
FERUNCODED1
sf.results.csv.gz


title: HEK293

description: bru-labeled RNA


title: FS46

description:
FER027
fertility.results.csv.gz


title: HCT116_UV

description: bru-labeled RNA

value: BruUV-seq


title: HCT116_r3

description:
HCT116 replicate 3
bru-labeled RNA


title: HCT116_r2

description:
HCT116 replicate 2
bru-labeled RNA


title: HCT116_r1

description:
HCT116 replicate 1
bru-labeled RNA


title: FS44

description:
FER024
sf.results.csv.gz


title: INDOLENT CLL [VB1183]

description:
VB1183
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

value: CD5+/CD19+ B cells

value: Chronic lymphocytic leukemia

value: 11q Del


title: FS41

description:
FER023
sf.results.csv.gz


title: FS32

description:
INF017
fertility.results.csv.gz, responder.results.csv.gz

value: responder


title: FS37

description:
INF018
fertility.results.csv.gz, responder.results.csv.gz


title: GM12891

description: bru-labeled RNA

value: 0.5 hours

value: bruseq


title: HF_r1

description:
HF replicate 1
bru-labeled RNA

value: 0 hours

value: Bromouridine (Bru)


title: CTRL [VB6131]

description:
VB6131
Small RNA expression profiling (tsRNAs and tRFs).
processed data file: CLL_tsRNA_normalized_data.txt
processed data file: CLL_tRF_normalized_data.txt

value: CD19+ B-cells


title: FS30

description:
FER015
sf.results.csv.gz


title: GM12878_UV

description: bru-labeled RNA


title: HAP1

description: bru-labeled RNA


title: GM12878_r2

description:
GM12878 replicate 2
bru-labeled RNA


title: FS28

description:
INF015
fertility.results.csv.gz


title: HEK293_UV

description: bru-labeled RNA


title: FS26

description:
INF012
fertility.results.csv.gz, responder.results.csv.gz


title: FS25

description:
FER022
sf.results.csv.gz


title: FS24

description:
INF020
sf.results.csv.gz


title: FS40

description:
INF019
fertility.results.csv.gz, responder.results.csv.gz

value: non-responder


title: BxPC3_UV

description: bru-labeled RNA


title: FS19

description:
FER019
sf.results.csv.gz


title: FS17

description:
FER020
fertility.results.csv.gz


title: csb

description: bru-labeled RNA

source_name: csb


title: BxPC3

description: bru-labeled RNA


title: A673_UV

description: bru-labeled RNA


title: A673

description: bru-labeled RNA


title: A375

description: bru-labeled RNA


title: FS12

description:
FER017
fertility.results.csv.gz


title: A2058_r2

description:
A2058 replicate 2
bru-labeled RNA


title: FS14

description:
FER016
sf.results.csv.gz


title: A2058_r1

description:
A2058 replicate 1
bru-labeled RNA


title: FS13

description:
FER018
fertility.results.csv.gz


title: IGR37

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

data_processing:
Files containing paired-end sequencing reads were mapped to human genome build hg19 using CLC Genomics Workbench software (CLC Bio)
Exon-aligned reads RPKM values were generated for differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: .txt containing feature counts and RPKM values

growth_protocol: Melanoma cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera). Melanocytes were supplemented with

extract_protocol:
Cells were grown to 80% confluence and harvested at room-temperature using the RNeasy mini kit (QIAGEN). Cells were scraped in PBS and lysed in Buffer RLT supplemented with 143 mM β-mercaptoethanol. The lysate was homogenised by being passed 10 times through a 0.9 mm needle and RNA purified on RNeasy spin columns, on-column DNase digestion was performed at room temperature for 15 minutes before being eluted in nuclease free water.
Library preparation and paired-end sequencing (RNA-Seq) was performed byHigh Throughput Genomics, Wellcome Trust Centre for Human Genetics, University of Oxford. A minimum depth of 40M mapped reads were generated per sample

value: melanoma


title: FS29

description:
INF016
fertility.results.csv.gz, responder.results.csv.gz


title: IGR39


title: FS8

description:
Resequencing of INF007
fertility.results.csv.gz


title: FS6

description:
FER010
fertility.results.csv.gz


title: HERMES

source_name: HERMES

value: melanocyte


title: FS7

description:
INF008
sf.results.csv.gz


title: FS3

description:
FER008
sf.results.csv.gz

value: fertile


title: FS1

description:
FER006
sf.results.csv.gz


title: FS4

description:
INF021
sf.results.csv.gz


title: sub_FER014_111231

description:
FER014
sf.results.csv.gz


title: sub_FER011_111118

description:
FER011
fertility.results.csv.gz

value: no


title: sub_FER012_111112

description:
FER012
fertility.results.csv.gz


title: sub_FER013_111215

description:
FER013
fertility.results.csv.gz


title: sub_FER009_109774

description:
FER009
sf.results.csv.gz

value: yes


title: sub_INF007_110386

description:
INF007
responder.results.csv.gz

value: infertile


title: DDstp-pknB_rep3: stp-pknB double mutant replicate 3

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

hyb_protocol: A mixture of RNA from WT or mutant strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

label: cyanine 3

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Newman Dstp-DpnkB

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in B medium

extract_protocol: Briefly, bacteria were lysed in 1 ml of Trizol reagent (Invitrogen Life Technologies, Karlsruhe, Germany) with 0.5 ml zirconia-silica beads (0.1 mm-diameter) in a high-speed homogenizer (Savant Instruments, Farmingdale, NY). RNA was isolated as described in the instructions provided by the manufacturer of Trizol. RNA isolation after phagocytosis was performed as described in the instructions provided by the manufacturer of the RNA isolation kit (ExpressArt RNAready, AmpTec) with the modification adding an inhibitor removal buffer (high pure viral nucleic acid kit, Roche diagnostics) in the first step. Then DNA digestion was performed as instructed by the RNA isolation kit.

treatment_protocol: no treatments

value: S. aureus strains grown in B medium

tag: genotype/variation

value: Dstp-DpnkB

label: cyanine 5

source_name: gDNA pool

value: Staphylococcus aureus gDNA mixture


title: DDstp-pknB_rep2: stp-pknB double mutant replicate 2


title: sub_INF009_110630

description:
INF009
fertility.results.csv.gz, responder.results.csv.gz


title: sub_INF006_110161

description:
INF006
fertility.results.csv.gz


title: Dstp_rep3: stp mutant replicate 3

source_name: Newman Dstp

value: Dstp


title: FS2

description:
FER007
sf.results.csv.gz


title: DpknB_rep3: pnkB mutant replicate 3

source_name: Newman DpnkB

value: DpnkB


title: DpknB_rep1: pnkB mutant replicate 1


title: SA_skin5

city: San Francisco

first: Tiffany

last: Scharschmidt

address: 513 Parnassus Ave, 1201B

department: Dermatology

institute: University of California, San Francisco

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and were aligned to UCSC GRCm38/mm10 reference genome with STAR software (2.4.2a)
SAM files were generated with SAMtools from alignment results
Read counts were obtained with htseq-count (0.6.1p1) with the union option
Differential expression was determined using the R/Bioconducter package DESeq2
Genome_build: Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: 060617_JLmerged_counts_SESAonly.csv: raw counts of sequencing reads
Supplementary_files_format_and_content: Results_SESAskin.csv: differential expression results from DESeq2

source_name: Whole skin

growth_protocol: Specific-pathogen-free newborn C57BL6 mice were colonized with either  Staphylococcus epidermidis Tü3298 or Staphylococcus aureus SF8300 starting on day 3 of life and every other day thereafter until post-natal day 19 by pipetting 100 μl of bacterial suspension onto their skin and distributing evenly using a sterile PBS-soaked cotton-tipped swab.

extract_protocol:
Whole skin RNA was isolated using an adapted protocol of the Qiagen RNeasy Fibrous tissue kit. In brief, tissue pieces were removed from RNA later and placed immediately in the suggested digestion buffer before dissociation using Miltenyi M tube. The kit protocol with column RNA isolation and DNAse cleanup was subseuqently followed. RNA quality was checked by Agilent Bioanalyzer Chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were sacrificed at 21 days of age and the entire trunk skin harvested and lightly defatted. An 8mm punch biopsy was taken from the back skin and placed in RNA later, kept overnight at 4C and then stored in -80 until subsequent RNA extraction.

value: Whole skin

tag: strain

tag: age

value: post natal day 21

tag: tissue source

value: skin

tag: bacteria

value: Staphyloccocus aureus


title: SA_skin4


title: sub_INF003_109631

description:
INF003
fertility.results.csv.gz, responder.results.csv.gz


title: Dstp_rep2: stp mutant replicate 2


title: sub_INF005_110041

description:
INF005
fertility.results.csv.gz, responder.results.csv.gz


title: sub_INF002_109618

description:
INF002
fertility.results.csv.gz, responder.results.csv.gz


title: WT_rep3: Wild type strains replicate 3

source_name: Newman WT

value: WT


title: GM12878_r1

description:
GM12878 replicate 1
bru-labeled RNA

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruseq

tag: time between end of bru labeling and rna extraction

value: 0 hours

tag: labeling agent

value: Bromouridine (Bru)


title: DDstp-pknB_rep1: stp-pknB double mutant replicate 1

tag: tissue


title: SA_skin3


title: SA_skin2


title: SUDHL1_SD36Me_24h_2

city: Memphis

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

description:
SD36Me_24h_116841
processed data file: LBAI_WANG_SUDHL1_STAT3_2019.csv

data_processing:
RTA version 1.18.66.3 (HCS version 2.2.68 ) was used for basecalling.
bcl2fastq version 2.17.1.14 was used for generation fastq files.
Read alignment was done using Bowtie v0.12.8, with parameters “-k 100”.
Gene abundance estimation was done using rSeq v0.2.2, with parameters “-expression_analysis”.
Transcriptome annotation: GENCODE v24 basic.
Genome_build: NCBI GRCh38.p5
Supplementary_files_format_and_content: RPKM values of each cell line treated with DMSO, SD36, SD36Me.

source_name: SU-DHL-1 cells

growth_protocol: Cells were grown in RPMI 1640 medium containing 10% fetal bovine serum, 50 units/mL penicillin and 100 µg/mL streptomycin and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were collected at the end of treatment and total RNA was purified using RNeasy Mini Kit from Qiagen. RNA was assessed for quality using the TapeStation (Agilent). Samples with RINs (RNA Integrity Numbers) of 8 or greater were ribosomal RNA depleted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
RNA libraries were prepared from the rRNA-depleted total RNA using TruSeq RNA Library Prep v2 kit (Illumina) following Illumina's standard protocol. Where the entire fraction of 0.1-3ug of rRNA depleted total RNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA were then adenylated and adapters were ligated. One of the adapters that was ligated had a 6 nucleotide barcode that was unique for each sample which allowed us to sequence more than one sample in each lane of a HiSeq flow cell (Illumina). The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit (Kapa Biosystems) for Illumina Sequencing platforms.

treatment_protocol: Cells were treated with DMSO (0.05% v/v), SD36 (1000 nmol/L) or SD36Me (1000 nmol/L) for 8 or 24 hours before collected for RNA isolation.

tag: cell line

tag: cell source

value: Lymph node

tag: genetic background

value: 88 chromosomes; t(2;5)(p23;q35) translocation

tag: molecular subtype

value: anaplastic large cell lymphoma

tag: treatment

tag: treatment duration


title: SUDHL1_SD36Me_24h_1

description:
SD36Me_24h_116840
processed data file: LBAI_WANG_SUDHL1_STAT3_2019.csv


title: SA_skin1


title: DpknB_rep2: pnkB mutant replicate 2

value: S. aureus strains grown in B medium


title: WT_rep1: Wild type strains replicate 1


title: SUDHL1_SD36_24h_2

description:
SD36_24h_116843
processed data file: LBAI_WANG_SUDHL1_STAT3_2019.csv